I wonder if there's any way to know for sure whether it is a Herx or gut irritation because that would really help me out. I did a two day fast last week which hopefully would have induced some healing in the gut and then began on the stomach acid straight after and immediately got a reaction, which might suggest a Herx. Who knows.
I'm just thinking perhaps one way of finding out could be by trying 'natural' antimicrobials? I haven't tried these yet but it's in the plan outlined by my doctor, after the antibiotics. In theory these shouldn't really be gut irritants considering they're natural products like oregano oil. If they give me the same sort of reaction to the acid then surely it's all likely to be a Herx reaction rather than gut irritation.